Im going to replace my AF7 for a Fenrir (if that is still the best sub £40 775 cooler?) However due to the hight i don't think my side fan will fit in the case.

Should I just remove the side fan or should I mount it externally to the case so it still blows onto the GPU?
Or will the Fan effect the cooling of the Fenrir as the edge of the fan will blow onto the top lower left side of the fenrir?

Side fans unless you have a serious overheating problem of chipset or GPU always seem to disrupt airflow for me, in every case i've built a system in. Holes,mesh, vents in the side are necessary then the GPU just draws cool air in itself, but a fan seems to cock everything up and things like the HDD's warm up. The P182 Antec case, possibly one of the most over-rated cases of all time is happy to let graphics cards boil simply because it has no side vents and pathetic airflow. I would try a fan but closely monitor temps.